Release Date



We expect this to be the final release version before transitioning to EMAN3. While some capabilities expected to be part of EMAN2 are available in some nascent forms here, this version is really just a continuation of recent developments in EMAN2, including major improvements to single particle and subtomogram averaging pipelines. This version also provides the ability to install EMAN2 as part of an existing Anaconda installation on your machine


This package contains EMAN2/SPARX/SPHIRE. We strongly suggest following the instructions: https://eman2.org/Install/BinaryInstallAnaconda/2.99 rather than just downloading and installing. There are alternative installation methods which may be better for your situation, and while simple, the instructions have important information.

Version changes

See the changelog: https://eman2.org/ChangeLog for a list of all major changes. Major improvements since EMAN2.91:

  • Fully functional GUI for Deep Learning GMM dynamics/variability analysis (PMC8363932).
    • GUI permits interactive exploration of manifold via Gaussians, and generation of arbitrary subclasses/3D maps.
    • New, less memory intensive approach can work with thousands of Gaussians and hundreds of thousands of particles.
    • Initial support for analysis of subtomogram variability.
  • New subtomogram averaging refinement program.
    • incorporates both 3-D, subtilt and defocus refinement.
    • Faster and better than the previous program.
  • New single particle refinement program with modest resolution improvement over historical approach. Produces per-particle orientations easier to compare with other software.
  • HDF5 compression with bit reduction
    • automatic for most workflows
    • support for bit reduction in non-HDF formats supporting external compression.
    • Significant file size reduction without information loss (PMID: 35724904).
    • Fixed minor problems with GUI on Macs, and native support for M1, M2, etc. Macs.
  • Updated support for new EER variants, and other file I/O improvements.
  • Many minor bugfixes.

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